Is it possible to force MIME::Parser to extract text-files on a Windows system without the extra CR's on the end of lines?

Probably not, but I wouldn't even bother looking :) grab Path::Tiny and/or File::Find::Rule find some target files and normalize the newlines to what you need them to be

update: OTOH, if you subclass MIME::Parser::FileUnder, you could normalize the newlines in "purgable"

So no it isn't possible to force MIME::Parser to do this with a setting but only with code